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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
1q0q NDP 1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1q0q NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 1.193
3anm NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.953
3anl NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.932
4gae NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic 1.1.1.267 0.811
1jvs NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 0.789
3au8 NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic 1.1.1.267 0.750
2jcv NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.735
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.735
3hwr NDP2-dehydropantoate 2-reductase / 0.724
4aic NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.724
1vi2 NADQuinate/shikimate dehydrogenase / 0.719
1wp4 NDP3-hydroxyisobutyrate dehydrogenase / 0.719
1i36 NAPConserved protein / 0.717
1yqd NAPSinapyl alcohol dehydrogenase / 0.713
5ein NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.711
3ras NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.710
2cvz NDP3-hydroxyisobutyrate dehydrogenase / 0.709
2i3g NAPN-acetyl-gamma-glutamyl-phosphate reductase 1.2.1.38 0.707
1m76 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.705
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.705
4lsm NADGlyceraldehyde-3-phosphate dehydrogenase / 0.705
1nbo NADGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.704
1nvm NADAcetaldehyde dehydrogenase 1.2.1.10 0.704
2jd0 NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.704
3adp NAILambda-crystallin 1.1.1.45 0.703
4p8r NADGlyceraldehyde-3-phosphate dehydrogenase / 0.703
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.702
1zh8 NAPUncharacterized protein / 0.701
1npd NADQuinate/shikimate dehydrogenase / 0.700
4oaq NDPR-specific carbonyl reductase / 0.698
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.697
5c7o NADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific 1.2.1.12 0.696
2q3e NAIUDP-glucose 6-dehydrogenase 1.1.1.22 0.695
2vhx NADAlanine dehydrogenase 1.4.1.1 0.695
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.695
1u8f NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.694
2ekp NAD2-deoxy-D-gluconate 3-dehydrogenase / 0.693
1vsv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.692
2ggs NDPdTDP-4-dehydrorhamnose reductase / 0.692
3a14 NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.692
4e5p NADPhosphonate dehydrogenase 1.20.1.1 0.692
4boy NADGlyceraldehyde-3-phosphate dehydrogenase / 0.691
3keq NADRedox-sensing transcriptional repressor Rex / 0.690
4y0k NAPAntE / 0.690
1hdg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.689
5a04 NDPGlucose-fructose oxidoreductase / 0.689
3ing NDPHomoserine dehydrogenase related protein / 0.687
4bkq NAIEnoyl-[acyl-carrier-protein] reductase [NADH] / 0.686
5dul NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.686
3ikt NADRedox-sensing transcriptional repressor Rex / 0.685
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.684
3t4e NADQuinate/shikimate dehydrogenase / 0.684
3wbb NAPMeso-diaminopimelate D-dehydrogenase / 0.683
1m75 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.681
3pef NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.681
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.680
3mvq NDPGlutamate dehydrogenase 1, mitochondrial 1.4.1.3 0.679
1pjc NADAlanine dehydrogenase / 0.678
2d2i NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.678
2vyv NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.677
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.677
2voj NADAlanine dehydrogenase 1.4.1.1 0.676
4eue NAITrans-2-enoyl-CoA reductase [NADH] / 0.676
3b20 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.674
2ep7 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.671
1dss NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.670
1fxs NAPGDP-L-fucose synthase / 0.670
2cy0 NAPShikimate dehydrogenase (NADP(+)) / 0.670
4o63 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.670
5eio NAP[LysW]-L-2-aminoadipate 6-phosphate reductase / 0.670
1cf2 NAPGlyceraldehyde-3-phosphate dehydrogenase / 0.669
4xr9 NADCalS8 / 0.669
3had NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.668
1yqx NAPSinapyl alcohol dehydrogenase / 0.667
4nu5 NADPhosphonate dehydrogenase 1.20.1.1 0.667
4y1b NAPAntE / 0.667
3tnl NADShikimate dehydrogenase (NADP(+)) / 0.665
3f3s NADLambda-crystallin homolog / 0.664
5a02 NAPGlucose-fructose oxidoreductase / 0.663
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.662
4oqy NDP(S)-imine reductase / 0.662
5a03 NDPGlucose-fructose oxidoreductase / 0.662
5aq1 NDPGlucose-6-phosphate 1-dehydrogenase / 0.662
3ket NADRedox-sensing transcriptional repressor Rex / 0.661
2glx NDP1,5-anhydro-D-fructose reductase / 0.660
1oaa NAPSepiapterin reductase 1.1.1.153 0.659
2dt5 NADRedox-sensing transcriptional repressor Rex / 0.659
2jcx NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.659
2yut NAPPutative short-chain oxidoreductase / 0.659
3w8f NAD3-hydroxybutyrate dehydrogenase / 0.659
1a7k NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.658
2gsd NADFormate dehydrogenase / 0.658
3hja NADGlyceraldehyde-3-phosphate dehydrogenase / 0.658
1h6a NDPGlucose--fructose oxidoreductase 1.1.99.28 0.657
3u4c NDPNADPH-dependent reductase BacG / 0.657
4okn NAIL-lactate dehydrogenase A chain 1.1.1.27 0.656
4z3d NDPCarbonyl reductase [NADPH] 1 1.1.1.184 0.656
1bsv NDPGDP-L-fucose synthase / 0.655
1yb5 NAPQuinone oxidoreductase 1.6.5.5 0.655
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.655
3tox NAPPutative oxidoreductase / 0.655
5ijz NAPNADP-specific glutamate dehydrogenase 1.4.1.4 0.655
1jn0 NDPGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic 1.2.1.13 0.654
4dbv NDPGlyceraldehyde-3-phosphate dehydrogenase / 0.654
2ixb NADAlpha-N-acetylgalactosaminidase 3.2.1.49 0.653
3keo NADRedox-sensing transcriptional repressor Rex / 0.653
3ntr NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.653
3ulk NDPKetol-acid reductoisomerase (NADP(+)) / 0.653
4e5m NAPPhosphonate dehydrogenase 1.20.1.1 0.653
5a05 NDPGlucose-fructose oxidoreductase / 0.653
1dbv NADGlyceraldehyde-3-phosphate dehydrogenase / 0.652
1dc6 NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.650
4bv9 NDPKetimine reductase mu-crystallin 1.5.1.25 0.650
4rcv NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase / 0.650